PDBsum entry 2civ

Oxidoreductase

PDB id: 2civ

Contents

Protein chain

299 a.a. *

Ligands

NAG-NAG-BMA

MAN-MAN

HEM

NAG ×2

MAN ×10

Metals

_BR ×5

_MN

Waters ×426

* Residue conservation analysis

PDB id:

2civ

Name:

Oxidoreductase

Title:

Chloroperoxidase bromide complex

Structure:

Chloroperoxidase. Chain: a. Fragment: residues 21-319. Synonym: chloride peroxidase, cpo. Ec: 1.11.1.10

Source:

Caldariomyces fumago. Organism_taxid: 5474. Other_details: leptoxyphium fumago

Resolution:

1.80Å R-factor: 0.160 R-free: 0.184

Authors:

K.Kuhnel,W.Blankenfeldt,J.Terner,I.Schlichting

Key ref:

K.Kühnel et al. (2006). Crystal structures of chloroperoxidase with its bound substrates and complexed with formate, acetate, and nitrate. J Biol Chem, 281, 23990-23998. PubMed id: 16790441 DOI: 10.1074/jbc.M603166200

Date:

26-Mar-06 Release date: 12-Jun-06

Protein chain

P04963  (PRXC_LEPFU) -  Chloroperoxidase from Leptoxyphium fumago

Seq: 373 a.a.

Struc: 299 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class: E.C.1.11.1.10 - chloride peroxidase.
• Reaction: RH + Cl^- + H2O2 = RCl + 2 H2O
• Cofactor: Heme

Heme (Bound ligand (Het Group name = HEM) matches with 95.45% similarity)

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1074/jbc.M603166200

J Biol Chem 281:23990-23998 (2006)

PubMed id: 16790441

Crystal structures of chloroperoxidase with its bound substrates and complexed with formate, acetate, and nitrate.

K.Kühnel, W.Blankenfeldt, J.Terner, I.Schlichting.

ABSTRACT

Chloroperoxidase (CPO) is a heme-thiolate enzyme that catalyzes hydrogen peroxide-dependent halogenation reactions. Structural data on substrate binding have not been available so far. CPO was therefore crystallized in the presence of iodide or bromide. One halide binding site was identified at the surface near a narrow channel that connects the surface with the heme. Two other halide binding sites were identified within and at the other end of this channel. Together, these sites suggest a pathway for access of halide anions to the active site. The structure of CPO complexed with its natural substrate cyclopentanedione was determined at a resolution of 1.8 A. This is the first example of a CPO structure with a bound organic substrate. In addition, structures of CPO bound with nitrate, acetate, and formate and of a ternary complex with dimethylsulfoxide (Me2SO) and cyanide were determined. These structures have implications for the mechanism of compound I formation. Before binding to the heme, the incoming hydrogen peroxide first interacts with Glu-183. The deprotonated Glu-183 abstracts a proton from hydrogen peroxide. The hydroperoxo-anion then binds at the heme, yielding compound 0. Glu-183 protonates the distal oxygen of compound 0, water is released, and compound I is formed.

Selected figure(s)

Figure 3.
FIGURE 3. Complexes of CPO with acetate, nitrate, and formate. A and B, acetate binds in two conformations at the active site (shown in light and dark gray). A second acetate molecule binds in the solvent channel near the iodide binding site. Two orientations rotated by 90° are shown. Final sigmaA-weighted 2mF[o] - DF[c] maps are shown with a contour level of 1 . C, CPO complexed with nitrate. An ethylene glycol molecule used as cryoprotectant is located above the nitrate. The ethylene glycol binds at the iodide specific binding site 3 and forms a hydrogen bond with Asn-74. D, complex of CPO with formate in the presence of ethylene glycol. A formate molecule is bound at the active site and forms hydrogen bonds with an ethylene glycol molecule. E, CPO-formate complex with a xylitol and sucrose-containing cryoprotectant. The formate binds in two orientations (shown in light and dark gray). F, solution spectra of CPO measured in the presence or absence of sodium formate and/or ethylene glycol. Measurements were done with solutions containing 0.06 mM CPO in 0.1 M sodium citrate, pH 3.6. Spectra were recorded at 20 °C with a path length of 1 mm using a ND-1000 spectrophotometer (NanoDrop Technologies Inc., Philadelphia, PA).

Figure 4.
FIGURE 4. Proposed mechanism of compound I formation catalyzed by chloroperoxidase.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2006, 281, 23990-23998) copyright 2006.

Figures were selected by an automated process.